bams2bam.py - merge genomic and transcriptome mapped bamfiles

Tags

Genomics NGS Geneset BAM Manipulation

Purpose

This script takes as input two BAM files from an RNASeq experiment. The first bam file (bamG) should contain reads mapped against the genome using a mapper permitting splicing (e.g. tophat). The second bam file (bamT) should contain reads mapped against known transcripts. This script will write a new bam file that removes reads from bamG that map to regions that are conflicting with those in bamT.

Note

Note that if junctions are supplied, the resultant bam files will not be sorted by position.

bamG

bam formatted file with reads mapped against the genome

bamT

bam formatted file with reads mapped against transcripts

Usage

Example:

python bams2bam.py bamT.bam bamG.bam

Type:

python bams2bam.py --help

for command line help.

Documentation

The script needs to look-up reads via their names. It thus builds an index of reads mapping

This script requires the NM attributes to be set. If it is not set, you will need to set a policy.

Command line options

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/cgat-apps/conda/latest/bin/cgat", line 11, in <module>
    sys.exit(main())
  File "/home/docs/checkouts/readthedocs.org/user_builds/cgat-apps/conda/latest/lib/python3.7/site-packages/cgat/cgat.py", line 132, in main
    module.main(sys.argv)
  File "/home/docs/checkouts/readthedocs.org/user_builds/cgat-apps/conda/latest/lib/python3.7/site-packages/cgat/tools/bams2bam.py", line 79, in main
    usage=globals()["__doc__"])
  File "/home/docs/checkouts/readthedocs.org/user_builds/cgat-apps/conda/latest/lib/python3.7/site-packages/cgatcore/experiment.py", line 510, in __init__
    **kwargs)
TypeError: __init__() got an unexpected keyword argument 'version'